AndreaGuarracino
commented
1 year ago Unfortunately, this is a known bug in our graph sorting algorithm in 1D that affects odgi viz visualizations. We still need to fix it somehow.
Andrea
From: henrivkgt @.> Sent: 16 March 2023 10:40 To: pangenome/odgi @.> Cc: Subscribed @.***> Subject: [pangenome/odgi] Odgi 1d visualization: understanding several drawn links to the very end of the image (Issue #487)
Hello,
I have been using odgi to visualize several pangenome graphs consisting of a handful of plant genomes, using both the 1d and 2d visualization. One thing that is unclear to me about the 1d visualization is the links drawn in many chromosome graphs, from seemingly repetitive regions towards the very last bin of the image. In the 2d visualization I can find no trace of these long-range connections, while the expected centromeric "tangle" does appear in both the 1d and the 2d visualization. The lines appear in graphs made both with pggb as well as with minigraph-cactus. I have attached two examples below of chromosome graphs where this happens. Could you shed some light on how this happens, or what is the meaning of these connections?
Best, Henri
[component 5 og 1d]https://user-images.githubusercontent.com/98946024/225668287-25b312cf-7e81-41d8-be99-c78a1390a541.png [component 2 og 1d]https://user-images.githubusercontent.com/98946024/225668326-65afb402-d5c3-458b-b627-30a062db96b3.png
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Hello,
I have been using odgi to visualize several pangenome graphs consisting of a handful of plant genomes, using both the 1d and 2d visualization. One thing that is unclear to me about the 1d visualization is the links drawn in many chromosome graphs, from seemingly repetitive regions towards the very last bin of the image. In the 2d visualization I can find no trace of these long-range connections, while the expected centromeric "tangle" does appear in both the 1d and the 2d visualization. The lines appear in graphs made both with pggb as well as with minigraph-cactus. I have attached two examples below of chromosome graphs where this happens. Could you shed some light on how this happens, or what is the meaning of these connections?
Best, Henri